Related Gene Expression Profiles Research Articles

Application of Sparse Representation in Bioinformatics.

Inspired by L1-norm minimization methods, such as basis pursuit, compressed sensing, and Lasso feature selection, in recent years, sparse representation shows up as a novel and potent data processing method and displays powerful superiority. Researchers have not only extended the sparse representation of a signal to image presentation, but also applied the sparsity of vectors to that of matrices. Moreover, sparse representation has been applied to pattern recognition with good results. Because of its multiple advantages, such as insensitivity to noise, strong robustness, less sensitivity to selected features, and no “overfitting” phenomenon, the application of sparse representation in bioinformatics should be studied further. This article reviews the development of sparse representation, and explains its applications in bioinformatics, namely the use of low-rank representation matrices to identify and study cancer molecules, low-rank sparse representations to analyze and process gene expression profiles, and an introduction to related cancers and gene expression profile database.

MammaPrint and BluePrint comprehensively capture the cancer hallmarks in early-stage breast cancer patients.

MammaPrint® (MP) is a 70‐gene signature that stratifies early‐stage breast cancer patients into low‐ and high risk of distant relapse. Further stratification of MP risk results identifies four risk subgroups, ultra‐low (UL), low, high 1, and high 2, with specific prognostic and predictive outcomes. BluePrint® (BP) is an 80‐gene signature that classifies breast tumors as basal, luminal, or HER2 molecular subtype. To gain insight into their biological significance, we annotated the MP 70‐ and BP 80‐genes with respect to the 10 hallmarks of cancer (HoC). Furthermore, we related gene expression profiles of the extreme ends of the MP low‐ and high‐risk patients (here called, ultra‐low (UL) and ultra‐high (UH) or High2, respectively), to the 10 HoC per BP subtype by differential gene expression and pathway analysis. MP and BP gene functions reflected all 10 HoCs. Most MP and BP genes were associated with sustaining proliferative signaling, followed by genome instability and mutation categories. Based on the gene expression profiles, UL and UH subgroup pathways were down ‐or upregulated, respectively, reflecting proliferative and metastatic features, such as G2M checkpoint, DNA repair, oxidative phosphorylation, immune invasion, PI3K/AKT/mTOR signaling, and hypoxia pathways. Notably, the UH HER2‐type was enriched in several immune signaling pathways, such as IL2/STAT5 signaling and TNFα signaling via NFκB. Our results show that MP and BP gene signatures represent and capture all 10 HoCs and highlight underlying biological processes of MP extreme samples, which might guide treatment decisions as the signature captures the full spectrum of early breast cancers.

GEPSdb: The Gene Expression Database of Poplar under Stress.

As a model tree species, poplar (Populus L.) has important economic and ecological value. Here, we constructed the GEPSdb (Gene Expression Database of Poplar under Stress; http://gepsdb.ahau-edu.cn/), which is an integrated database of poplar gene expression profiles derived from RNA-seq and microarray library data. This database provides a comprehensive collection of gene expression data from poplar exposed to 14 types of environmental stress from 11 high-quality RNA-seq experiments and 51 microarray libraries. The GEPSdb includes 56 genes from previous literature that have been examined in poplar and functionally verified. By incorporating data from numerous expression analyses, GEPSdb provides a user-friendly web interface for querying, browsing, and visualizing the expression profiles of related genes. Consequently, GEPSdb can be used to link transcription data with phenotypes and can enhance our understanding of important biological processes and mechanisms underlying complex agronomic traits in poplar.

Abstract 11641: Targeted Intrathecal Nos1 Inhibition Rescues Pulmonary Hypertension and Right Ventricular Failure in Rats by Reducing Neuroinflammation, Apoptosis and Sympathoexcitation

Introduction: Pulmonary hypertension (PH) is associated with aberrant sympathoexcitation leading to RV failure (RVF), arrhythmias and death. NOS1 is known to induce neuroinflammation, nitrosative stress and apoptosis in neural tissue. In spinal cord, NOS1 is activated by afferent signaling via Ca 2+ influx through activated NMDAR in dorsal horn by increased glutamate release via K + channels. Hypothesis: Cardiopulmonary afferent signaling in PH-RVF leads to NOS1-mediated neuroinflammation, nitrosative stress and apoptosis in thoracic spinal cord (TSC) resulting in aberrant sympathoexcitation. Targeted intrathecal NOS1-inhibition may rescue PH and RVF. Methods: Male rats received s.c. Monocrotaline (MCT, 60mg/kg, n=8, 4wk) or Sugen (SuHx, 20mg/kg, n=8, 3wk hypoxia+2wk normoxia). Controls received PBS (n=8). A group of MCT-rats received either daily intrathecal specific NOS1-inhibitor S-Methyl-L-thiocitrulline (SMTC; 0.5mg/kg, n=7) or PBS (n=7) from day 14-28. Echo and RV cath were performed. TSC and RV RNASeq, RT-qPCR, NOS1 activity, NOS1 immunolocalization, microglia+astrocyte quantification and TUNEL were performed. Plasma catecholamines were measured by ELISA. Values are mean±SD. Results: Rats developed severe PH-RVF (Increased RVSP, Fulton-index, decreased RVFAC; p<0.01). TSC transcriptome showed common genes and pathways linked to neuroinflammation, nitrosative stress and apoptosis and identified NOS1 as one of the top-most upregulated genes (MCT / SuHx:8 fold; p<0.05) in TSC but not lumbar. We found significantly increased microglia+astrocyte activation, NMDAR-1, Kv3.4, CX3CL1, nitrosative stress markers AP1B1, AP1M1 and pro-apoptotic p53, TGFβ1 expression in TSC. We observed increased NOS1 activity, its colocalization with microglia+astrocyte, apoptosis and norepi/epi in both models. SMTC decreased RVSP, Fulton-index, RVID d , pulmonary vascular wall thickness, increased RVFAC by reducing TSC NOS1 activity, CX3CL1/TGF β 1, microglia/astrocyte activation, apoptosis and plasma norepi/epi (p<0.05). RV transcriptome demonstrated that SMTC decreased pro-fibrotic, pro-apoptotic, SNS & RAAS related and pro-inflammatory RV gene expression profile. Conclusions: Intrathecal NOS1 inhibition rescues PH and RVF.

Characterization of Flavonoids and Transcripts Involved in Their Biosynthesis in Different Organs of Cissus rotundifolia Lam.

Cissus rotundifolia Lam. is used as a medicinal herb and vegetable. Flavonoids are the major components for the therapeutic effects. However, flavonoids constituents and expression profiles of related genes in C. rotundifolia organs are unknown. Colorimetric assay showed the highest flavonoid concentration in roots compared to the stem and leaf. Widely target-based metabolome analysis allowed tentative identification of 199 compounds in three organs. Flavonols and flavones were the dominant flavonoids subclasses. Among the metabolites, 171 were common in the three organs. Unique accumulation profile was observed in the root while the stem and leaf exhibited relatively similar patterns. In the root, six unique compounds (jaceosidin, licoagrochalcone D, 8-prenylkaempferol, hesperetin 7-O-(6″malonyl) glucoside, aureusidin, apigenin-4′-O-rhamnoside) that are used for medicinal purposes were detected. In total, 18,427 expressed genes were identified from transcriptome of the three organs covering about 60% of annotated genes in C. rotundifolia genome. Fourteen gene families, including 52 members involved in the main pathway of flavonoids biosynthesis, were identified. Their expression could be found in at least one organ. Most of the genes were highly expressed in roots compared to other organs, coinciding with the metabolites profile. The findings provide fundamental data for exploration of metabolites biosynthesis in C. rotundifolia and diversification of parts used for medicinal purposes.

Anthocyanin Accumulation and Related Gene Expression Profile in ‘Red Zaosu’ Pear and Its Green Mutant

Red-skinned pear is a promising commercial fruit due to its attractive appearance and nutritious value. Anthocyanin is the determinant of the red coloration of the pear peel. However, differences in anthocyanin accumulation exist among red pear cultivars with different genetic backgrounds. In this study, we analyzed the anthocyanin content and gene expression patterns in the fruits and different tissues of the red pear ‘Red Zaosu’ at different developmental stages and found a difference in anthocyanin accumulation between ‘Red Zaosu’ pear and its green mutant. The data showed that the expression profiles of transcripts that encoded critical anthocyanin biosynthetic genes were basically consistent with a tendency to a decreased anthocyanin content during fruit development, indicating that a synergistic effect of these genes was responsible for anthocyanin biosynthesis and regulation. Tissue-specific expression analysis of anthocyanin biosynthetic genes showed that they could be expressed in all tissues but at different levels. PbF3H, PbDFR, and PbANS were mainly expressed during the early flowering period, which explained the reduced levels of anthocyanin content in petals. Additionally, the content of anthocyanins and the expression levels of PbDFR, PbANS, and PbMYB10 significantly decreased in the green mutant of ‘Red Zaosu’, suggesting that PbDFR, PbANS, and PbMYB10 probably play a decisive role in determining the skin coloration of ‘Red Zaosu’ and its green mutant.

Menghai Huangye, a novel albino tea germplasm with high theanine content and a high catechin index

Yunnan Province has a very wide diversity of tea germplasm resources. A variety of special tea germplasms with outstanding traits have been discovered, including tea germplasms with high anthocyanin content and low caffeine content. Albino tea cultivars generally have higher contents of theanine that contribute to the umami taste, and the quality of tea brewed from it is higher. The catechin index (CI), the ratio of dihydroxylated catechins (DIC) to trihydroxylated catechins (TRIC), is a crucial index of suitability for processing tea. In this study, the albino tea plant Menghai Huangye (MHHY) with yellow leaves was identified. Analysis of the biochemical components revealed that MHHY was enriched in theanine and the total catechins (TC) were lower than Yunkang 10 (YK10). In addition, the CI value of MHHY was extremely significantly higher than that of YK10. Metabolic profile of catechins and the related gene expression profile analysis found that the coordinated expression of the key branch genes F3′H and F3′5′Ha for the synthesis of DIC and TRIC in tea plant was closely related to the high CI and low TC of MHHY. Further analysis of the F3′H promoter showed that a 284-bp deletion mutation was present in the F3′H promoter of MHHY, containing the binding sites of the transcriptional repressor MYB4 involved in flavonoid metabolism, which might be an important reason for the up-regulated expression of F3′H in MHHY. Overall, this study provides a theoretical basis for understanding the characteristics of albino tea germplasm resources and efficiently utilizing high-CI tea germplasm resources.

Suppressive effects of gecko cathelicidin on biofilm formation and cariogenic virulence factors of Streptococcus mutans

ObjectiveThe aims of this study were to investigate the effectivity of gecko cathelicidin Gj-CATH2 on biofilm formation and cariogenic virulence factors of S. mutans, and preliminary explore its function mechanisms. DesignMinimum inhibitory concentration and bacterial killing kinetics assays were performed to assess the antimicrobial effect of Gj-CATH2.The influence of Gj-CATH2 on S. mutans biofilm formation was determined by crystal violet staining method and observed by SEM. The effects of Gj-CATH2 on exopolysaccharides (EPS) synthesis, bacterial aggregation, acidogenicity and aciduricity of S. mutans were also investigated. Quantitative real-time PCR was conducted to acquire the expression profile of related genes. ResultsGj-CATH2 showed strong bactericidal and anti-biofilm effects on S. mutans. SEM confirmed the reduction of the dense structure in S. mutans biofilm in Gj-CATH2-treated groups. Gj-CATH2 significantly inhibited EPS synthesis, cell aggregation, acid production of S. mutans, but showed no influence on its acid proof. Furthermore, the expression of genes related to biofilm formation (gtfB/C/D, gbpB/D), quorum sensing system (luxS and comD/E) and acidogenicity (ldh) was significantly suppressed by Gj-CATH2. Gj-CATH2 also displayed advantageous resistance in human saliva and exhibited negligible toxicity against mammalian cells. ConclusionsGj-CATH2 inhibited S. mutans biofilm formation by targeting the bacterial adhesion and the biofilm maturation stages. Gj-CATH2 significantly suppressed virulence factors production of S. mutans, resulting in decreased EPS synthesis and reduced acidogenicity of bacteria. These findings suggest Gj-CATH2 might be a promising agent for clinical application in prevention of dental caries.

Cyclin-dependent kinase 1 shows to be a potential genetic target for chemical cystitis.

BackgroundIn the present study, we aimed to explore whether common genetic targets or signaling pathways existed in chemical cystitis.MethodsGene Expression Omnibus (GEO) database was used to search the related gene expression profiles. The differentially expressed genes (DEGs) were identified by using GEO2R. The DAVID 6.8 Beta and R software were used to perform Kyoto Encyclopedia of Genes and Genomes pathway analysis and Gene Ontology function analysis of DEGs. The protein‐protein interaction network was constructed by STRING 11.0 to reveal the potential gene interactions. The expression of cyclin‐dependent kinase 1 (Cdk1) at the messnger RNA (mRNA) and protein levels was examined by real‐time polymerase chain reaction (PCR) and Western blot analysis analysis, respectively.ResultsThe GEO database was searched, and the gene expression profiles of GSE55986 and GSE68539 were downloaded. A total of 262 DEGs and 356 DEGs were identified from GSE55986 and GSE68539, respectively. We found that the p53 signaling pathway might play a key role in the development of chemical cystitis, and Cdk1 acted as a crucial gene in the p53 signaling pathway. Moreover, the experimental results of real‐time PCR and Western blot analysis analysis demonstrated that the expression of Cdk1 at the mRNA and protein levels in cystitis tissues was significantly increased in different animal models of chemical cystitis compared with the control group.ConclusionCdk1 might be a potential pathogenic genetic target for chemical cystitis.

Effects of Plant Sterols Intake on Systematic and Tissue Specific Lipid Metabolism in C57BL/6J Mice

Abstract Objectives To investigate the effects of plant sterols intake on systematic and tissue specific lipid metabolism in C57BL/6J mice. Methods Male C57BL/6J mice were randomly divided into control diet group (CS) and plant sterol group (PS, 2% plant sterols). After 28 weeks of continuous feeding, the serum of the mice were collected for biochemical and mass spectrometry tests. Serum levels of total cholesterol (TC), triglyceride (TG) and free sterols were determined. The livers and lungs were collected for free sterol quantification and RNA-seq analysis. Results Compared with the CS group, 2% plant sterols intake significantly reduced the levels of TC in the serum of mice (P < 0.05), with the TG level unchanged. The quantitative results of free sterols showed that the concentration of campesterol were increased, and the cholestanol levels were decreased significantly in the serum and liver of the PS group mice. The results of RNA-seq analysis were used to further evaluate its impact on the lipid metabolism related gene expression profile in the livers and lungs. The results showed that HMGCR, SQLE, HMGCS1, SREBF1, and other genes related to cholesterol synthesis in the PS group were significantly up-regulated in the liver, but not in the lung; Among the first 20 targeting pathways related to the action of plant sterols, the liver differentially expressed genes were enriched in lipid metabolism (steroid biosynthesis, terpenoid skeleton biosynthesis, peroxisome, bile acid secretion, PPAR, MAPK, fatty acid metabolism.), inflammation related (Cell adhesion molecules, leukocyte trans-endothelial migration) and amino acid metabolism (glutathione, valine, leucine and isoleucine metabolism). The differential genes in lung tissue are enriched in lipid metabolism (acetone metabolism, fatty acid metabolism, insulin resistance, terpenoid skeleton biosynthesis, iron death, PPAR), cell function (internal Swallowing, aging) and vascular smooth muscle contraction etc. Conclusions Differentially expressed gene networks reflect the multi-dimensional regulation of plant sterols on tissue specific lipid metabolism, which lays a good foundation for further revealing its mechanism. Funding Sources Yihaikerry Nutrition and Food Safety Foundation, Chinese Nutrition Society; Project of Technology Innovation and Application, Chongqing, China

POS0398 ADIPONECTIN INDUCES SYNOVIAL ANGIOGENESIS IN RHEUMATOID ARTHRITIS THROUGH METABOLIC REMODELING

Background:Our team have previously reported that Adiponectin correlates well with synovial inflammation and progressive bone erosion in rheumatoid arthritis (RA). Angiogenesis is another important part, which plays a critical role in the pathogenesis of RA.Objectives:We hypothesized that adiponectin induces synovial angiogenesis in RA.Methods:Single-cell RNA sequencing (scRNA-Seq) was used to screen cellular changes in local knee joint of collagen-induced arthritis (CIA) after intraarticularly injected of adiponectin. Chimera models of synovium-cartilage-NOD/SCID mice, matrigel plug assay and rat aortic ring assay were performed to demonstrate the pro-angiogenesis role of adiponectin. Cellular experiment, including proliferation, migration, apoptosis, tube formation and angiogenesis related gene expression profile, were detected with Human Umbilical Vein Endothelial Cells (HUVEC) and Mice Lung Microvessel Endothelial Cell (MLMEC) after adiponectin stimulation. Seahorse was performed to clear the influence of adiponectin to cell metabolism.Results:The synovium and pannus hyperplasia worse in CIA model after intraarticularly injected of adiponectin, along with more serious synovitis and bone erosion. ScRNA-Seq of synovial tissues separated from CIA reminded that endothelial cell barbarically grows via metabolic remodeling after stimulated with adiponectin. Synovial chimera, matrigel plug and rat aortic ring shows adiponectin accelerates angiogenesis significantly in different background conditions. In vitro, endothelial cell proliferation detecting by RCTA and CCK8, migration by wound healing and transwell, apoptosis by FACS, tube formation and angiogenesis related gene expression profile by PCR-ARRAY were promoted by adiponectin in both HUVEC and MLMEC. Seahorse showed HUVEC made more use of glycolysis after co-cultured with adiponectin, a method of cell energy supply that tumor cells possess called warburg effect, that drives endothelial cell hyperplasia in severe environment.Conclusion:As a classic metabolic regulator, adiponectin exacerbates CIA by promoting angiogenesis through metabolic remodeling. The findings not only provide a novel insight into the pathogenic role of adiponectin, but also reveals a potential therapeutical strategy to attenuate revascularization in RA.Disclosure of Interests:None declared

Differential expression of Notch related genes in dental pulp stem cells and stem cells isolated from apical papilla

Although dental pulp and apical papilla are originated from neural crest cells, these tissues exhibit distinct characteristics. Notch signaling is one of the known signaling pathways regulating stemness and behaviors of stem cells. The aim of this study was to examine Notch signaling related gene expression profile comparing between coronal pulp tissues and apical pulp complex. Results demonstrated that coronal pulp tissue had higher expression levels of various genes in Notch pathway. However, NOTCH2, MAML2, DTX4, and NEDD4 mRNA levels were significantly lower in coronal pulp tissue than those of apical pulp complex. Furthermore, dental pulp stem cells (DPSCs) and stem cells isolated from apical papilla (SCAPs) were isolated and characterized. These two cell types exhibited similar mesenchymal stem cell surface markers. DPSCs expressed higher mRNA levels of NOTCH3, NOTCH4, DLL1, and HES1. In addition, SCAPs demonstrated higher colony formation and cell proliferation than DPSCs. In summary, cells and tissues from dental pulp and apical papilla exhibited the distinct gene expression profile of Notch related genes. This could be of one the signaling participated in control of DPSCs and SCAPs cells behaviors.

Reversible plasticity in brain size, behaviour and physiology characterizes caste transitions in a socially flexible ant (Harpegnathos saltator).

Phenotypic plasticity allows organisms to respond to changing environments throughout their lifetime, but these changes are rarely reversible. Exceptions occur in relatively long-lived vertebrate species that exhibit seasonal plasticity in brain size, although similar changes have not been identified in short-lived species, such as insects. Here, we investigate brain plasticity in reproductive workers of the ant Harpegnathos saltator. Unlike most ant species, workers of H. saltator are capable of sexual reproduction, and they compete in a dominance tournament to establish a group of reproductive workers, termed 'gamergates'. We demonstrated that, compared to foragers, gamergates exhibited a 19% reduction in brain volume in addition to significant differences in behaviour, ovarian status, venom production, cuticular hydrocarbon profile, and expression profiles of related genes. In experimentally manipulated gamergates, 6-8 weeks after being reverted back to non-reproductive status their phenotypes shifted to the forager phenotype across all traits we measured, including brain volume, a trait in which changes were previously shown to be irreversible in honeybees and Drosophila. Brain plasticity in H. saltator is therefore more similar to that found in some long-lived vertebrates that display reversible changes in brain volume throughout their lifetimes.

Single-Molecule Long-Read Sequencing of Purslane (Portulaca oleracea) and Differential Gene Expression Related with Biosynthesis of Unsaturated Fatty Acids

This study aimed to obtain the full-length transcriptome of purslane (Portulaca oleracea); assorted plant samples were used for single-molecule real-time (SMRT) sequencing. Based on SMRT, functional annotation of transcripts, transcript factors (TFs) analysis, simple sequence repeat analysis and long non-coding RNAs (LncRNAs) prediction were accomplished. Total 15.33-GB reads were produced; with 9,350,222 subreads and the average length of subreads, 1640 bp was counted. With 99.99% accuracy, after clustering, 132,536 transcripts and 78,559 genes were detected. All unique SMART transcripts were annotated in seven functional databases. 4180 TFs (including transcript regulators) and 7289 LncRNAs were predicted. The results of RNA-seq were confirmed with qRT–PCR analysis. Illumina sequencing of leaves and roots of two purslane genotypes was carried out. Amounts of differential expression genes and related KEGG pathways were found. The expression profiles of related genes in the biosynthesis of unsaturated fatty acids pathway in leaves and roots of two genotypes of purslane were analyzed. Differential expression of genes in this pathway built the foundation of ω-3 fatty acid accumulation in different organs and genotypes of purslane. The aforementioned results provide sequence information and may be a valuable resource for whole-genome sequencing of purslane in the future.

Role of digestive protease enzymes and related genes in host plant adaptation of a polyphagous pest, Spodoptera frugiperda.

The evolutionary success of phytophagous insects depends on their ability to efficiently exploit plants as a source of energy for survival. Herbivorous insects largely depend on the efficiency, flexibility, and diversity of their digestive physiology and sophistication of their detoxification system to use chemically diverse host plants as food sources. The fall armyworm, Spodoptera frugiperda (J.E. Smith), is a polyphagous pest of many commercially important crops. To elucidate the ability of this insect pest to adapt to host plant mechanisms, we evaluated the impact of primary (corn) and alternate (rice) host plants after 11 generations on gut digestive enzymatic activity and expression profiles of related genes. Results indicated that the total protease and class-specific trypsin- and chymotrypsin-like protease activity of S. frugiperda significantly differed among host plant treatments. The class-specific protease profiles greatly differed in S. frugiperda midguts upon larval exposure to different treatments with inhibitors compared with treatments without inhibitors. Similarly, the single and cumulative effects of the enzyme-specific inhibitors TLCK, TPCK, and E-64 significantly increased larval mortality and reduced larval growth/mass across different plant treatments. Furthermore, the quantitative reverse transcription polymerase chain reaction results revealed increased transcription of two trypsin (SfTry-3, SfTry-7) and one chymotrypsin gene (Sfchym-9), which indicated that they have roles in host plant adaptation. Knockdown of these genes resulted in significantly reduced mRNA expression levels of the trypsin genes. This was related to the increased mortality observed in treatments compared with the dsRED control. This result indicates possible roles of S. frugiperda gut digestive enzymes and related genes in host plant adaptation.

Evaluating the Impact of Post-Emergence Weed Control in Honeybee Colonies Located in Different Agricultural Surroundings.

Simple SummaryThe honeybee Apis mellifera is one of the main pollinators in agricultural ecosystems and therefore they are exposed to pesticides and the reduction of floral diversity. Cytochrome P450 monooxygenases are enzymes involved in xenobiotic detoxification used by organisms, including insects. In this study, we evaluated honeybee foraging activity and the expression profiles of several cytochromes, before and after the administration of a mixture of three of the most used herbicides in the region during the summer season. Additionally, we investigated whether colonies located in three distinct agricultural environments with different crop/wild flora proportions are affected similarly or differently by herbicide administration. We found that the expression of several cytochrome P450 genes decreased significantly in larvae after post-emergence weed control and they showed significant differences between apiaries in the case of honeybee workers. Besides, we found significant positive correlations between pollen collection and some pesticide detoxification genes. Our results support that diversity and quality of resource availability as well as the presence of herbicides affect colonies’ nutritional state and bee health. Moreover, their detoxification response shows that larvae are more harmed than adults in these agricultural ecosystems.The honeybee Apis mellifera is exposed to agricultural intensification, which leads to an improved reliance upon pesticide use and the reduction of floral diversity. In the present study, we assess the changes in the colony activity and the expression profile of genes involved in xenobiotic detoxification in larvae and adult honeybees from three apiaries located in agricultural environments that differ in their proportion of the crop/wild flora. We evaluated these variables before and after the administration of a mixture of three herbicides during the summer season. The expression of several cytochrome P450 monooxygenases decreased significantly in larvae after post-emergence weed control and showed significant differences between apiaries in the case of honeybee workers. Principal component analysis (PCA) revealed that colonies located in the plot near to a wetland area exhibited a different relative gene expression profile after herbicide application compared with the other plots. Moreover, we found significant positive correlations between pollen collection and the pesticide detoxification genes that discriminated between plots in the PCA. Our results suggest that nutrition may modify herbicide impact on honeybees and that larvae are more harmed than adults in agroecosystems, a factor that will alter the colonies’ population growth at the end of the blooming period.

Role of Biogenic Silver Nanoparticles on Hyperhydricity Reversion in Dianthus chinensis L. an In Vitro Model Culture

Hyperhydricity (HH) is one of the major problems in plant tissue culture. Increased frequency (75%) of HH in the cultures of. Dianthus chinensis L. cultivar telstar scarlet raised from nodal segments on agar (0.85%) gelled, benzyladenine (2.5 µM) supplemented Murashige and Skoog (MS) medium was noticed in the third subculture onwards. To reduce HH and to resume normal growth, the addition of silver nitrate is routinely recommended in the culture medium. However, the impact of biogenic silver nanoparticles (AgNPs) on HH reversion has not been well investigated. In this study, biogenic AgNPs prepared from leaf extract of D. chinensis were used to control HH in D. chinensis cultures. The characterization of bioynthesized AgNPs has been done by UV–Vis spectroscopy, Fourier transform infrared spectroscopy, X-ray diffraction analysis, energy-dispersive X-ray spectrum, transmission electron microscopy, and atomic force microscopy. Higher water content or addition of ethylene precursor, ethephon, in culture medium induced plantlet with unhealthy, pale green, glassy shoots (HH). Due to the biological activity of Ag+ ions and water regulating mechanism, AgNPs treatment on hyperhydric explant (4 weeks) resulted in high retroversion coupled with reduced relative water content. Supplementation of 100 µg L−1 AgNPs in MS medium significantly reduced the percentage of HH to 13.3%, in contrast to control (100%). Addition of AgNPs effectively reduced hydrogen peroxide (H2O2) content (50%) characterized by green, healthy shoots with proper stomata in contrast to hyperhydric shoots. The gene expression pattern of 1-aminocyclopropane-1-carboxylase synthase (ACS1) and 1-aminocyclopropane-1-carboxylic acid oxidase (ACO1) showed reduced expression after the retroversion of microshoots in 100 µg L−1 AgNPs medium compared to hyperhydric shoot. The relative gene expression profile of ACS1 and ACO1 at 100 µg L−1 AgNPs treatment was 9.8 and 1.8-fold over normal shoots (1), respectively. Inter simple sequence repeat (ISSR) analysis on AgNPs directed HH reverted shoots showed genetic stability thus proved safe to adopt this technique to produce true to type plants. Combined manipulation, coordination of water permeability, and anti-ethylene activity of AgNPs were responsible for effective HH reversion. These finding will put forward the future utilization of bioencapsulated AgNPs in plant tissue culture and agriculture practices.

Analysis of Immune Gene Expression in Seabass (Lates calcarifer) Immunized with Inactivated Vaccine against Similar Damselfish Virus

Background: Control of viral disease outbreaks in aquaculture and minimizing the loss of production can be achieved by development of effective vaccines. Efficacy of these vaccines can be improved by using adjuvants, immunostimulants or vaccine carriers. In this study, inactivated similar damselfish virus (SRDV) vaccine was prepared and expression profiles of immune related genes against virus challenge of the vaccine were investigated in seabass (Lates calcarifer). Methods: Formalin-inactivated virus vaccine was developed to assess its immune responses to SRDV challenge in fish. The immune response was induced by intra-peritoneal injection with inactivated viral vaccine added Quil-A® adjuvant. The transcriptional levels of immune genes IRF-7 and IL-10 were evaluated in the spleen and kidney of seabass from different groups by quantitative real-time RT-PCR assays. Result: Expression profiles of both genes (IRF-7 and IL-10) in the kidney and spleen of seabass immunized with vaccine added adjuvant were up-regulated at 48 hpi of the virus. In comparison, spleen of seabass immunized with vaccine added adjuvant showed highest expression profiles than kidney. The current study provides evidence for the presence of expression profiles of immune-related genes during the SRDV infection. The study also strongly suggests that Quil-A® adjuvant enhances the immune response of the vaccine candidates.

Effects of hypoxia on the mRNA expressions of TRAIL-mediated cell death related genes in hypoxia-tolerant rodent (Nannospalax nehringi) and some characteristics of these proteins

The aim of the present study was to determine the mRNA expression profiles of TRAIL-mediated cell death related genes of the hypoxia-tolerant rodent Nannospalax nehringi under hypoxia. The nucleotide and amino acid sequences of these genes were identified. Captured Nannospalax nehringi were randomly divided into normoxia and hypoxia groups. The hypoxia group was exposed to a 7% O2 + 93% N2 gas mixture for 52 h, while animals in the normoxia group were housed under normoxic conditions. Total RNAs were isolated from brain and lung tissues. The cIAP-1, cIAP-2, XIAP, DcR1, DcR2, FLIP and OPG genes were PCR amplified, and the cIAP-1, cIAP-2, XIAP, OPG, TRAIL and FLIP genes were sequenced. Sequenced genes were translated into amino acid sequences and compared with reliable sequences of closely similar species. The genes in the brain were regulated for protection against hypoxia; however, the genes in the lung were regulated differently. Many mutations and insertions were observed on the conserved regions of the cIAP-1, cIAP-2, XIAP, OPG and TRAIL genes in N. nehringi. We propose that these gene mutations and insertions contribute to the anti-hypoxic properties of N. nehringi.

Transcriptome-metabolome analysis of fatty acid of Bamei pork and Gansu Black pork in China.

To study the difference in transcriptome level of fatty acid metabolism pathway in Bamei pork and the difference of pork quality caused by the difference. In this study, Bamei pigs breeding in Huzhu farm of QingHai province were selected as the test object, compared with Gansu Black pigs. Four indexes of nutmeg acid (DX1), palmitic acid (DX2), stearic acid (DX3) and linoleic acid (DX4) were set. The expression profiles of fat metabolism related genes between the two groups samples were analysed by GCMS metabolomics and transcriptomics, then coexpression network analysis were conducted to obtain phenotypic related genes. The results showed that the metabolic levels of DX3 and DX4 were significantly higher than those of other fatty acids. Among these differences, the ENSSSCG00000024681 (G1) and ENSSSCG00000036883 (G2) genes play important regulatory roles in fatty acid metabolism, and the upregulated expression of their gene obviously affects the level of fatty acid metabolism, thereby affecting the quality and taste of pork. In addition, we found that there was a good correlation between the same lines, and the genetic traits of the hybrid lines of Bamei pig and Black pig are more inclined to Bamei pig. In the independent fatty acid metabolism, "Mg2+"and flavin adenine dinucleotide are more active, which plays an important role in energy utilization. Therefore, we can be inferred that the metabolism of stearic acid and linoleic acid are important fatty acids for pork quality. It also further confirms that the research method of combined omics is of great significance for the study of species traits and gene functions.